Re: [Freesurfer] mri_surf2surf

Try this instead: mri_surf2surf --srcsubject $SUBJECT --sval-xyz $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --trgsubject ico --tval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --tval-xyz --hemi lh It is admittedly a little obtuse. mri_surf2surf was originally programmed to accept sur

[Freesurfer] creating a custom overlay

Hi, I'm wondering whether it is possible to create an overlay consisting of a subset of clusters from a sig.mgh file, filtered according to custom criteria and preserving the significance value of each vertex in the remaining clusters so that the overlay can be thresholded as I choose.

Re: [Freesurfer] Problem make_average_subject

The problem is that it is calling mris_preproc with --srcsurfreg, and you do not have the version of mris_preproc that accepts this flag. You can edit it to make it --surfreg. Or, you can get a new copy of make_average_surface from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve

[Freesurfer] freesurfer version difference

Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for the other subjects. Will there be a difference between both the versions. We are comparing individual subjects brain (aseg stats) at 2 different instances. It so happens we are comparing the same subject's b

[Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs

Dear FS experts, 1. There are some frequent mismatches between the white matter and cortex parcellations (aparc+aseg.mgz and wmparc.mgz) with zeroed voxels between them. Would suppressing the option --ribbon when running aparc2aseg either during cortex or white matter parcellation (or both) resul

Re: [Freesurfer] SPGR format

you might try -it ge or -it gelx doug [EMAIL PROTECTED] wrote: Is it a dicom? Try mri_convert -i 12461.spgr -o 12461.mgz -it dicom It did not work either, unfortunately. - Anders doug [EMAIL PROTECTED] wrote: What's your cmd line and what exactly is the problem? doug

Re: [Freesurfer] SPGR format

> you might try -it ge or -it gelx Thanks for the tips. We have tried both without luck, unfortunately. - Anders > > doug > > [EMAIL PROTECTED] wrote: > >>>Is it a dicom? Try >>> >>>mri_convert -i 12461.spgr -o 12461.mgz -it dicom >>> >>> >> >> >>It did not work either, unfortunately. >> >>- And

Re: [Freesurfer] freesurfer version difference

Hi Mithra, yes, there might be. You should rerun the 4.0.0 subjects with 4.0.1 (it should preserve all manual edits so you won't need to intervene). cheers, Bruce On Mon, 11 Feb 2008, Mithra wrote: Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for

Re: [Freesurfer] freesurfer version difference

Mithra, We highly recommend using the same version of freesurfer to perform recon-all processing on a group of subjects. Processing with different versions introduces an extra level of variability in your study. However, in looking at the ReleaseNotes page: https://surfer.nmr.mgh.harvard.edu/fs

Re: [Freesurfer] SPGR format

> Is it a dicom? Try > > mri_convert -i 12461.spgr -o 12461.mgz -it dicom It did not work either, unfortunately. - Anders > > doug > > > > [EMAIL PROTECTED] wrote: > >>>What's your cmd line and what exactly is the problem? >>> >>>doug >>> >>> >> >>Hi, the commands and problems are pasted below.

Re: [Freesurfer] creating a custom overlay

Have you tried mri_surfcluster? Bruce Fischl wrote: Hi Cate, is doing it manually an option? You could draw closed curves around each cluster, or click in each one and use the custom fill in tksurfer. Is that what you mean? Bruce On Mon, 11 Feb 2008, Catherine Hartley wrote: Hi, I'm

Re: [Freesurfer] creating a custom overlay

Hi Cate, is doing it manually an option? You could draw closed curves around each cluster, or click in each one and use the custom fill in tksurfer. Is that what you mean? Bruce On Mon, 11 Feb 2008, Catherine Hartley wrote: Hi, I'm wondering whether it is possible to create an overlay c

[Freesurfer] recon-all with DICOM vs. mgz inputs - volume differences

On the freesurfer wiki, it says that recon-all can be done with DICOM inputs in addition to mgz inputs. In doing recon-all using DICOM or mgz (created via unpacksdcmdir), the volumetric values obtained using mris_volume and mris_wm_volume are different. For example in one subject, with DICOM inpu

Re: [Freesurfer] recon-all with DICOM vs. mgz inputs - volume differences

Jennifer, I think what you are seeing is due to randomness in some of the freesurfer algorithms, as dicom files are converted to mgz during the -i step (which need only be included once) and should itself not account for differences. You can include the flag -norandomness to recon-all which fixes

Re: [Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs

Hi Luis, 1. I'll leave this for Doug. 2. The aseg.mgz is indendent of (and produced before) the mri_segment step (which produces the wm.mgz). In general we don't use the cortical part of the aseg as the surfaces in our experience are more accurate. 3. Can you give an example of this? I would th